Variant report

Variant	rs6594588
Chromosome Location	chr5:111658754-111658755
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111654503..111657162-chr5:111657627..111659825,2	K562	blood:

Extended variants
information (count: 150 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10037824	1.00[ASN][1000 genomes]
rs10040749	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10054560	1.00[ASN][1000 genomes]
rs10065740	1.00[ASN][1000 genomes]
rs10068493	1.00[ASN][1000 genomes]
rs10069011	1.00[ASN][1000 genomes]
rs10070995	1.00[ASN][1000 genomes]
rs1020951	1.00[ASN][1000 genomes]
rs10463433	0.93[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477478	1.00[ASN][1000 genomes]
rs10478073	1.00[ASN][1000 genomes]
rs1054724	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1078128	1.00[ASN][1000 genomes]
rs11241153	1.00[ASN][1000 genomes]
rs11241160	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186685	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12187589	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187787	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs12187819	1.00[ASN][1000 genomes]
rs12187850	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12188700	1.00[ASN][1000 genomes]
rs12189034	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12189437	0.86[GIH][hapmap]
rs13153601	1.00[ASN][1000 genomes]
rs1318178	1.00[ASN][1000 genomes]
rs1366144	1.00[ASN][1000 genomes]
rs1427978	1.00[ASN][1000 genomes]
rs1524425	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1554624	0.93[CEU][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs1560052	1.00[ASN][1000 genomes]
rs1560053	1.00[ASN][1000 genomes]
rs1560054	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1560055	1.00[ASN][1000 genomes]
rs1560057	1.00[ASN][1000 genomes]
rs1560058	1.00[ASN][1000 genomes]
rs1560061	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17134319	0.93[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17134321	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17134327	0.93[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17134348	0.93[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271934	0.93[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17343994	1.00[ASN][1000 genomes]
rs17345175	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs17354763	1.00[ASN][1000 genomes]
rs17354833	1.00[ASN][1000 genomes]
rs1896620	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1896621	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975015	1.00[ASN][1000 genomes]
rs2067096	1.00[ASN][1000 genomes]
rs2114991	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2416277	1.00[ASN][1000 genomes]
rs386446	1.00[ASN][1000 genomes]
rs4292487	1.00[ASN][1000 genomes]
rs4602685	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4957632	1.00[ASN][1000 genomes]
rs4957634	1.00[ASN][1000 genomes]
rs4957636	1.00[ASN][1000 genomes]
rs4958002	1.00[ASN][1000 genomes]
rs4958003	1.00[ASN][1000 genomes]
rs4958004	1.00[ASN][1000 genomes]
rs4958009	1.00[ASN][1000 genomes]
rs4958010	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4958012	1.00[ASN][1000 genomes]
rs4958013	1.00[ASN][1000 genomes]
rs4958014	1.00[ASN][1000 genomes]
rs4958015	1.00[ASN][1000 genomes]
rs4958020	1.00[ASN][1000 genomes]
rs4958025	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs55637388	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55639430	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55650579	1.00[ASN][1000 genomes]
rs55712004	1.00[ASN][1000 genomes]
rs55796748	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55814486	1.00[ASN][1000 genomes]
rs55829200	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55845736	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55913426	1.00[ASN][1000 genomes]
rs56108405	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56288086	1.00[ASN][1000 genomes]
rs56293447	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307310	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56881711	1.00[ASN][1000 genomes]
rs57428532	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59537089	1.00[ASN][1000 genomes]
rs60636568	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61061658	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365251	1.00[ASN][1000 genomes]
rs62365255	1.00[ASN][1000 genomes]
rs62367266	1.00[ASN][1000 genomes]
rs62372421	1.00[ASN][1000 genomes]
rs6594566	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6594567	1.00[ASN][1000 genomes]
rs6594569	1.00[ASN][1000 genomes]
rs6594571	1.00[ASN][1000 genomes]
rs6594574	1.00[ASN][1000 genomes]
rs6594577	1.00[ASN][1000 genomes]
rs66521031	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66550707	1.00[ASN][1000 genomes]
rs66814803	1.00[ASN][1000 genomes]
rs66892745	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67033649	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67586008	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67631852	1.00[ASN][1000 genomes]
rs6863063	1.00[ASN][1000 genomes]
rs6872947	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6876893	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6878117	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs6878423	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6884589	1.00[ASN][1000 genomes]
rs6893877	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6894036	0.93[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894358	1.00[EUR][1000 genomes]
rs72781655	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72781664	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72781668	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72781676	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72781677	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72781678	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783609	0.83[EUR][1000 genomes]
rs72783628	1.00[ASN][1000 genomes]
rs72783634	1.00[ASN][1000 genomes]
rs7703522	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7704087	1.00[ASN][1000 genomes]
rs7706160	1.00[ASN][1000 genomes]
rs7709484	1.00[ASN][1000 genomes]
rs7710973	1.00[ASN][1000 genomes]
rs7711158	1.00[ASN][1000 genomes]
rs7714258	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7716309	1.00[ASN][1000 genomes]
rs7716394	1.00[CEU][hapmap]
rs7717160	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7717363	1.00[ASN][1000 genomes]
rs7719346	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7722291	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821736	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821738	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs821739	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs821746	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs821749	0.93[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890757	1.00[ASN][1000 genomes]
rs890758	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1021530	chr5:111626266-111683317	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1028181	chr5:111628901-111683317	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv882714	chr5:111655382-111807579	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6594588	SNORA13	cis	parietal	SCAN
rs6594588	CDO1	cis	cerebellum	SCAN
rs6594588	EPB41L4A	cis	Skin Sun Exposed Lower leg	GTEx
rs6594588	APOL4	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111637400-111684600	Weak transcription	Aorta	Aorta
2	chr5:111650600-111659600	Enhancers	Fetal Heart	heart
3	chr5:111652800-111665200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:111652800-111666800	Weak transcription	Right Ventricle	heart
5	chr5:111652800-111667000	Weak transcription	Esophagus	oesophagus
6	chr5:111653200-111674000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:111657000-111665200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:111658600-111665400	Weak transcription	Lung	lung
9	chr5:111658600-111666800	Weak transcription	Left Ventricle	heart

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